[gmx-users] conversion of the AMBER parameters to GROMACS with negative barrier height values

[Justin Lemkul]

On 9/23/14 1:18 PM, ABEL Stephane 175950 wrote:
> Hello all,
>
> I am trying to convert some GLYCAM parameters to do simulations with the GROMACS code. In the glycam force field, several dihedral terms have negative barrier height values, for instance, -20 in the following parameter:
>
>   Os-Cj-Cj-Ha   1  -20.00          0.0             2          SCEE=1.0 SCNB=1.0 copy of Os-Ck-Ck-Ha
>
> So I wonder if  It is safe to use a negative value in case of GROMACS  for the amplitude
>
> ;i   j	 k   l	     func  phi0	   cp	       mult
>   Os-Cj-Cj-Ha   9     0.0     -83.680    2
>
> Sorry if it is a stupid question and thanks in advance for your response
>

Do a single-point energy evaluation in both programs and confirm that it is correct.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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